The Analysis Clinic · For researchers and faculty

Something about your analysis is being questioned. Let's work out why.

Reviewers ask for analyses that don't fit. Study sections doubt the power analysis. Models fail to converge, and results contradict the literature. Each Case in the Clinic explains what the symptom means, what usually causes it, which checks to run, and how to explain the decision.

What are you dealing with? ↓ Ask about your analysis →
01
Recognize the symptom
Match what you're seeing to what usually causes it.
02
Run the right checks
Short, concrete diagnostics, not a methods textbook.
03
Compare defensible options
What each fix assumes, and what it costs you.
04
Write the response
Language you can adapt for a reviewer, editor, or study section.
Start with the problem

What are you dealing with?

Choose the problem closest to yours to narrow the cases below.

A reviewer or editor challenged my analysis

Post hoc power · multiplicity · model choice

Browse 3 cases →

My grant needs a defensible power analysis

Pilot data · ICCs · attrition

Browse 2 cases →

My model won't run

Convergence · random effects · estimation

Browse 2 cases →

My results don't make sense

Sign flips · suppression · interactions

Browse 2 cases →

My data aren't what we planned

Missing data · clusters · measurement

Browse 1 cases →

We can't reproduce our own results

Reproducibility · software · workflow

Browse 1 cases →
Diagnosed and ready to read

11 Cases, each with reproducible R and Python scripts.

These educational cases use synthetic data, simulations, or specified numerical illustrations. They are not client case reports. Check each case’s assumptions before applying its approach to your study.

Case 001 · Diagnosed
A reviewer or editor challenged my analysis

Reviewer 2 Asked for a Post Hoc Power Analysis

Why "observed power" can't answer the reviewer's real question, and the three analyses that can.

Power analysisEquivalence testingR
Case 002 · Diagnosed
A reviewer or editor challenged my analysis

The Reviewer Wants a Multiple-Comparisons Correction

Whether to correct depends on the claim you're making, not on how many p-values are in the paper.

Multiple testingHolmFalse discovery rateR
Case 003 · Diagnosed
My grant needs a defensible power analysis

Can I Power My Grant on My Pilot's Effect Size?

Small pilots give effect sizes too noisy to plan on, and the pilots that look most promising are the most misleading.

Power analysisPilot studiesGrant writingR
Case 004 · Diagnosed
A reviewer or editor challenged my analysis

Reviewer: “Why Didn’t You Use a Multilevel Model?”

Choose an analysis that respects the unit of assignment and dependence, then show what changes in the inference.

Clustered dataMixed modelsR
Case 005 · Diagnosed
My grant needs a defensible power analysis

Powering a Cluster-Randomized Grant When the ICC Is Unknown

Show how the required number of clusters changes across plausible ICCs, and separate participant attrition from cluster loss.

Cluster designsPower analysisGrant writingR
Case 006 · Diagnosed
My model won't run

My Mixed Model Won’t Converge with Crossed Random Effects

Separate numerical trouble, boundary estimates, and unsupported random slopes before changing the model.

Mixed modelsConvergencelme4R
Case 007 · Diagnosed
My results don't make sense

The Effect Flipped Sign When I Added a Covariate

Check the analysis rows and the adjustment question before treating a sign reversal as evidence of a mistake.

RegressionCovariate adjustmentR
Case 008 · Diagnosed
My data aren't what we planned

Missing Data Across Waves: What Will Reviewers Accept?

Make the missing-data assumptions visible, choose a method that matches the study, and show sensitivity to departures from MAR.

Missing dataLongitudinal studiesmiceR
Case 009 · Diagnosed
We can't reproduce our own results

My Coauthor Reran the Code and Got Different Results

Trace the first point of divergence in inputs, analysis rows, coding, and software before comparing final p-values.

ReproducibilityResearch workflowR
Case 010 · Diagnosed
My model won't run

My Logistic Regression Has Separation

Investigate perfect prediction before interpreting huge odds ratios or treating an optimizer’s last iterate as an estimate.

Logistic regressionSeparationRPython
Case 011 · Diagnosed
My results don't make sense

My Interaction Is Significant—What Do I Report?

Translate the interaction into planned slopes and contrasts, with uncertainty on the scale your research question needs.

InteractionsRegressionReportingRPython

Satisfying a reviewer isn't the same as fixing the analysis.

A quick fix can make a warning disappear or a comment go away while leaving the inference weaker than before. Each Case explains what the problem means for your conclusions, compares the defensible responses, and gives you wording you can adapt. Every number comes from an R script you can download and run.

Working on a dissertation? Dissertation Stats Helper's Analysis Clinic covers the problems doctoral students meet most. Preparing a manuscript? Reviewer Ready reviews the statistics before you submit.

Organize the problem before changing the analysis

Record your question, warning or reviewer comment, checks attempted, and next decision in the free troubleshooting worksheet.

Open the printable worksheet →

Still stuck after the first checks?

Some problems turn on the details of your design, data, or the exact reviewer comment. A free 30-minute consult can identify the next defensible step and what it would take.

Describe your research question, data structure, what you have tried, and any reviewer or committee concern. Include your deadline. Please leave out participant records and confidential information.

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